BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 048122
(125 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T3T|A Chain A, Structure Of Formylglycinamide Synthetase
pdb|3UJN|A Chain A, Formyl Glycinamide Ribonucleotide Amidotransferase From
Salmonella Typhimurium : Role Of The Atp Complexation
And Glutaminase Domain In Catalytic Coupling
pdb|3UMM|A Chain A, Formylglycinamide Ribonucleotide Amidotransferase From
Salmonella Typhimurium: Role Of The Atp Complexation And
Glutaminase Domain In Catalytic Coupling
Length = 1303
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 11 ARKWQKLAAIRQKRIMSTIFKG-DDAEKCYV 40
A +W+++AA R+M T+F DAEK ++
Sbjct: 129 AEQWRQVAAELHDRMMETVFSSLTDAEKLFI 159
>pdb|3UGJ|A Chain A, Formyl Glycinamide Ribonucletide Amidotransferase From
Salmonella Typhimurum: Role Of The Atp Complexation And
Glutaminase Domain In Catalytic Coupling
Length = 1303
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 11 ARKWQKLAAIRQKRIMSTIFKG-DDAEKCYV 40
A +W+++AA R+M T+F DAEK ++
Sbjct: 129 AEQWRQVAAELHDRMMETVFSSLTDAEKLFI 159
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEK 37
+ T+ L + R W ++A Q R++ TI K D E+
Sbjct: 604 VITRGLEIVRRDWSEIAKETQARVLETILKHGDVEE 639
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ + K D EK
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKA 639
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ + K D EK
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKA 639
>pdb|2QPX|A Chain A, Crystal Structure Of Putative Metal-Dependent Hydrolase
(Yp_805737.1) From Lactobacillus Casei Atcc 334 At 1.40
A Resolution
Length = 376
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 15/36 (41%)
Query: 67 QALLELAEEFGLPTNGPLTVLCDTAFMEYVVTLISH 102
L LA+EF L N PL D + Y + H
Sbjct: 57 HGFLALAKEFALDANNPLAAXNDPGYATYNHRIFGH 92
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ I K D E+
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEA 639
>pdb|2OZV|A Chain A, Crystal Structure Of A Predicted O-methyltransferase,
Protein Atu636 From Agrobacterium Tumefaciens.
pdb|2OZV|B Chain B, Crystal Structure Of A Predicted O-methyltransferase,
Protein Atu636 From Agrobacterium Tumefaciens
Length = 260
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 88 CDTAFMEYVVTLISHNVNEDAERPLLTLIAGS 119
C + F +TLI EDA R L+T I GS
Sbjct: 182 CGSRFGGLEITLIHPRPGEDAVRXLVTAIKGS 213
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ I K D E+
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEA 639
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ I K D E+
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEA 639
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ I K D E+
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEA 639
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ I K D E+
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEA 639
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ I K D E+
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEA 639
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
+ T+ L + R W ++A Q R++ TI K D E+
Sbjct: 604 VITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEA 640
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
I+T+ L + R W ++A Q R++ I K D E+
Sbjct: 603 ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEA 639
>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AHC|B Chain B, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AIL|C Chain C, Crystal Structure Of An Evolved Replicating Dna Polymerase
Length = 775
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 2 ISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKC 38
+ T+ L + R W ++A Q R++ TI K D E+
Sbjct: 604 VITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEA 640
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.135 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,044,362
Number of Sequences: 62578
Number of extensions: 92258
Number of successful extensions: 144
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 130
Number of HSP's gapped (non-prelim): 16
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)